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Life, Tomorrow's Comprehension

September 21, 2007

Proposed Definitions Of Earth Life, Organism And Gene

http://www.physforum.com/index.php?showtopic=14988&st=225&#entry346136

Earth Life: 1. a format of temporarily constrained energy, retained in temporary constrained genetic energy packages in forms of genes, genomes and organisms 2. a real virtual affair that pops in and out of existence in its matrix, which is the energy constrained in Earth's biosphere.

Earth organism: a temporary self-replicable constrained-energy genetic system that supports and maintains Earth's biosphere by maintenance of genes.

Gene: a primal Earth's organism.

Suggesting,

Dov Henis

========================================

Life, Tomorrow's Comprehension

Science-Informed View Of The Universe, Life, "God" And Religion

Chapter I

Life, A Real Virtual Affair, Its Drive And Purpose

A. Life's Fractal Evolution

The observation of the CBF1 switch, from

http://www.physorg.com/news107357572.html

contributes to my view of the following major fractal chronological several-10^8-years macro layers of Life's evolution:

1 – Individual independent genes evolve into cooperative interdependent gene aggregates.

2 – The outer cell's membrane (OCM) evolves as the first and major multi-functional organ of the gene aggregates/genomes.

3 – Individual cells evolve into symbiotic systems.

4 – Evolution of multicellular organisms.

The biggest hindrance of scientific, and even technological, progress in comprehension and exploitation of Biology is the avoidance to accept-regard genes-genomes as organisms. And equally hindering is the lack of a term for genes-genome that explicitly and clearly defines them as organisms, as The Prime Cardinal Earth Life Organisms, distinguished from all cellular secondary stratum organisms.

This avoidance, which is fraught with implications about the nature of life, is also the biggest hindrance of human existential and social progress.

B. Viruses, Too, Are Bona Fide Organisms

Evolution is always in the direction of more effective survivability; however, this is not always in the direction of more complexing for coping with changing environments and competition.

In a stable nutritious environment, like in Earth's oceans, coping with vital requirenments, evolution, is in the opposite direction, simplify tooling and means.

It is plain common sense that viruses, even Viroids and Virusoids, nothing more than single strands of DNA or RNA, sometimes only 200-300 nucleotides long, are organisms as alive as we are, evolved at life genesis era and selected for survival in forms, composition and capabilities by living, and even replicating, off their richer kin. Smart little buggers.

C. Evolution-Survival Rediscovered

Quoting from "Aging And Genetics" at

http://www.physorg.com/news107180970.html

"genes associated with longevity also became more common in each succeeding cohort. These results indicate that the frequency of deleterious genotypes may increase among people who live to extremely old ages because their protective genes allow these disease-related genes to accumulate,”

It appears that Evolution and Selection For Survival have just been re-discovered.

When when when will "scientists" and "science literature editors" get it through their scientific skulls that the source of our (and others species') individuals' uniqueness is the genome's polymorphisms, which come about from polymorphisms of its member genes.

It is about time that "scientists" make the Life Evolution mental leap, that they swallow and digest the revelation that a genome is a living complex organism consisting of (by now) interdependent symbiotic living member genes.

D. Cells Are Not Organisms

It irritates me again and again when unscientific science editors allow reference to cells as organisms. Cells are the spaceships, the edifices, that house the genomes, THE organisms. Scientifically cells are NOT organisms. The outer cell membrane is an organ. Plain and simple.

A possible explanation of this scientific ignorance is our still incomplete knowledge of the nature of the constituents of the cells' contents and of the functions of the outer-cell-membrane , the multifunctional organ of the genome, coupled with misty comprehension of the nature of life.

Cellular membranes and cells' contents are evolution products of the in-cell organisms, the genomes. Continued reference to cells as organisms is a gross anachronism that brakes/slows developement of life sciences.

E. Drive and Purpose of Life

Cognition = the capability, process or act of thinking, questioning and analysing.

Cognition is Cultural, is Biological. Cognition derives from culture, which is a biological attribute of ALL organisms regardless of size or complexity.

Culture = the totality of ways of the organisms' dealing with (reaction to, manipulation of, exploitation of) its environment.

The choice and promotion of our purpose in life derives solely from our cognition.

F. Encyclopedia of Life (EOL)

I read some time ago that biologist E.O. Wilson has a new project, The Encyclopedia of Life (EOL), aiming to make all knowledge of the world's 1.8 million known species freely available online within just 10 years.

I suggest that this would be a waste of effort and of time, because it would most probably be based on the presently accepted tree of life, with one thing branching off after another, we f.e. listed under genus Homo species sapien, genus being a grouping of one or more related and morphologically similar species.

I suggest that in the age of Genetics and DNA identification and definitions of genes expressions phylogeny should be redefined and reorganized based on the evolution of the genetic material, as the tree of life should present comprehension of how the genetic material has been evolving on Earth since four billion yrs ago…

The differences between the trees of life based on the classical "descriptive" taxonomy or on genetics would be great and of great consequences.

A genetic-based tree would not only correct several wrong "placings" and throw light on and bring to view yet undiscovered junctions-relationships of genera, but I posit that – most important – the comprehension that ALL LIFE EVOLUTION is the evolution of genes/genes-associations since four billion yrs ago, I posit that this comprehension might have a radical influence on the cognition and culture of humans and on their implications in personal and societal life organizations.

G. Life's Drive and Purpose

1. If one accepts, intuitively and logically, Pasteur's observation that all life must come from previously existing life, then the answer to "what makes a mono- and poly-cell life-form a Life" is the answer to "what makes some molecular associations in cells LIVES", and vice versa. It is the "lifehood" of genes that makes us and all other forms of life on Earth living organisms, and evolution has been the route of Life's ever more complexing progress since the first replication of the first gene.

Early independent peptides, primordial genes, have entered into symbiotic associations in which eventually each of the ever increasing host of functions/tasks vital for the evolving associations is taken up by the member most efficient at it, leading to gene speciation and to gene
specialization.

The history of life begins with independent genes, cascading fractally from single independent genes to agregate of genes, then to agregate of agregate of genes. Cooperative association is an inherent feature of life throughout all its evolution and at all its levels, in pre-cell and in mono-cell life and in mono-cell communities and in poly-cell life-forms and in communities of poly-cell life forms.

2. The totality of life in Earth's biosphere (the outermost part of the planet's shell — including air, land, surface rocks and water — within which life occurs, and which biotic processes in turn alter or transform. Wikipedia.) is a temporary grand store of energy, and all living organisms are elaborate temporary energy storage containers and all base genetic materials are "Life quanta", carriers of "Life photons". Humans are just one of the many types of Earth's living organisms, regardless of the reason and purpose of their self-inflated high-self-esteem.

3. Life's evolution has been and still is and will continue to be the evolution of genes. The total number of defined genes, each with its own unique identity/functional-capability is, of course, the number of organisms' species multiplied by their number of genes, which are now dependent-symbiotic members in chromosomes, cooperative-communes of genes. It is the GENES that evolve, and the evolution of the chromosomes and of 'higher strata' organisms is simply a consequence of their genes' evolution. The drive and purpose of evolution of the organisms is to enhance the functionality and survivability of the genes, in order to maintain and enhance Earth's biosphere energy storage.

4. This is the plain bare story of the drive and purpose of life. We do not yet comprehend what ENERGY is generically. We are just beginning to comprehend the nature of the raw material called Life and that the purpose of OUR life is ours to choose and develop and follow.

Again, humans, like every other organism, are just products of evolution of the individual and collective genes of their genome. And humans, like every other organism, repay their genetic formers with feedbacks that serve to further complex their formers and to increase their formers' survivability. The 'higher-strata' organisms are only means of survival of THE PURPOSE of life, which is their genetic material. However, as far as the organism is concerned it itself IS the purpose of life; ask any human…

H. Earth Life Is A Real Virtual Affair

Earth Life Is A Real Virtual Affair; it pops in and out of existence in its matrix, which is the energy constrained in Earth's biosphere .

I. Tree of Life

1. In Biology Online, 26-28 Nov 2006, AG asks:

How is the Tree of Life rooted?… What could the last universal common ancestor be?

Dov suggests http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q–?cq=1&p=194

2. Scientism and "evolutionary thinking" suggest that the study of the nature of life must be focused on the nature of the presently known earliest genes and on the probable nature of their probable earlier editions, backwards to the treshold of formation-transition of pre-RNA molecules into their self-replicating RNA editions, in the company of their precursors and of the predecessors of the precursors.

3. Most probable conjecture of the constellation of the Stealthy Life Genesis:

(a) In a (need composition definition) aqueous medium are present all components of the early "replicating configurations" plus all the predecessors of those components, and

(b) the energy balance of each of the progressing (steps) reactions, along the direction from the base elements level up to the replicator, are always forward-favoured, so that in the presence of all the required elements the replicator's formation energetically draws the progressive reactions.

The starting clues are, of course, the earliest available replicating compositions and their in-cell processes, and the starting unknown variables are the systems' base molecules and the systems' energetic circumstances.

(c) The essential early events of the energy-contents-driven "chemicals-to-life" progression comprise single-strand base extensions and ligations. DNA formation occurs most probably very much later.

All the consecutive steps in the progression are energy-contents-driven. Thus the chemicals-to-life transit is not a single dramatic step/rung of the ladder but consists of multi-small-steps/rungs and, due to variations in circumstances and in-line with the fractal nature of everything in the environments, it is random/stochastic.

(d) I conjecture life's genesis much earlier than the celling of genes. Genomes are communal coops of what way back originally were RNA independent genes, these various/different genes being then the first proliferrable life forms. Evolution and survival directed them and their much younger DNA progeny to become united, chromosomes and genomes, simply because cooperation is the most survivable mode, and the further process of evolution included celling for control of environmental parameters plus ever increasing member genes specialization as more capabilities evolve by some individual members of the commune of genes.

4. AG : I was also leaning toward Woese's theory

Dov : Genesis Of Life

Carl Woese ( June 9, 1998 ):

"The ancestor ( of life ) cannot have been a particular organism, a single organismal lineage. It was communal (13, 22), a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn become the three primary lines of descent".

Dov Henis:

Earth life's genesis cannot have been cell(s). Cells, liken all (every) objects and processes and natural laws in the universe, are – since singularity – products of evolution and are continuously further evolving. Everything in the cosmos is fractal, rehappens on many scales, and is continuously evolving. Each and every system in the universe continuously evolves within the total universal evolution and all the systems' evolutions are intertwined. Thus the root of earth's life cannot have been deus-ex-machina cells. Cells cannot have been but one of the forms of products of evolution of energy-transformation-storage systems, since at the beginning was the energy singularity, at the end will be near zero mass and an infinite dispersion of the beginning energy, and in-between, the universe undergoes continuous evolution consisting of myriad energy-to-energy and energy-to-mass-to-energy transformations. Therefore the roots of earth-life's genesis must have been much earlier than the celling of genes, in cosmic phenomena of active temporary reservoirs or pockets or bubbles of energy, on Earth in formation of individual RNA replicating genes.

end chapter I

———————————-

Chapter II

Natural Selection Is A Two Level Interdependent Affair

1) Evolution ensues from genome/genes modifications ("mutations"), inherently ever more of them as new functional options arise for the organism.

2) Modifications of genome's functional capabilities can be explained by the second-stratum organism's culture-life-experience feedbacks to its genome, its prime/base organism. The route-modification selection of a replicating gene, when it is at its alternative-splicing-steps junctions, is biased by the feedback gained by the genome, the parent organism, from the culture-life-experience of its progeny big organism. THIS IS HOW EVOLUTION COMES ABOUT.

3) The challenge now is to figure out the detailed seperate steps involved in introducing and impressing the big organism's exp
eriences (culture) feedbacks on its founding parents' genome's genes, followed by the detailed seperate steps involved in biasing-directing the genes to prefer-select the biased-favored splicing.

4) I find it astonishing that only very few persons, non-professional as well as professional biologists-evolutionists, have the clear conception that selection for survival occurs on two interdependent levels – (a) during the life of the second-stratum progeny organism in its environment, and (b) during the life of its genome, which is also an organism. Most, if not all, persons think – incorrectly – that evolution is about randomly occurring genes-genome modifications ("mutations") followed with selection by survival of the progeny organism in its environment. Whereas actually evolution is the interdependent , interactive and interenhencing selection at both the two above levels.

end chapter II

———————————

Chapter III

The Cosmic Drive and Purpose

Behind

The Drive and Purpose Of Life

(1) Again, Earth Life Is A Real Virtual Affair; it pops in and out of existence from its matrix, which is the energy constrained in Earth's biosphere .

The totality of life in Earth's biosphere (the outermost part of the planet's shell — including air, land, surface rocks and water — within which life occurs, and which biotic processes in turn alter or transform. Wikipedia.) is a temporary grand store of constrained energy, and all living organisms are elaborate temporary energy storage containers and all base genetic materials are "Life quanta", carriers of "Life photons".

(2) Singularity (max density) and D-Infinity (max expansion/ cosmic energy dilution) are the two cosmic stable states. Their in-between is a metastable state, which is an everyday commonsense observation. Likewise is the observation that the denser the compacting goal of material the more energy is required, and vice versa the more thorough the disintegration of material the higher the amount of energy released. It seems that E=mC^2 is a specific case of the cosmic (and universal) process

E=Total[m(1+D)] where D is the Distance from Big Bang point and the sum is of all spatial values of D from D=0 to D=selected value.

[BTW, (Nov 9 2006), following Newton (1) gravity is decreased when mass is decreased and (2) acceleration of a body is given by dividing the force acting upon it by its mass. By plain common sense the combination of those two 'laws' may explain the accelerating cosmic expansion of galaxy clusters, based on the above E/ m/ D suggested relationship.]

(3) Since the Universe, including its sub-systems, also Life, is a continuously evolving fractal system, ergo energy is the base element of everything and individual genes are the base elements of Life. Cosmic evolution is evolution of energy, and within it Life's evolution is the evolution of the genes/energy-quanta carriers.

At the beginning was the energy singularity. At the end will be near zero mass and an infinite dispersion of the beginning energy. In-between, the universe undergoes continuous evolution, consisting of myriad energy-to-energy and energy-to-mass-to-energy transformations.

The cosmos evolution process comprises, though, phenomena of forms of temporary energy storage pockets, energy dispersion constraints. Examples of such temporary pockets are black holes of all sizes, and all forms of biospheres if/wherever they are.

The temporary constrained energy pockets are far-removed versions, up-fractionally evolved, scattered cosmic fragmants of singularity-akin energy sources. Energy stored in the temporary constrained energy pockets resists dispersion; we do not yet comprehend why and how. However, we comprehend that we, all Earth life, are real virtual products formed by Earth's biosphere energy for maintaining Earth's biosphere bio as long as possible.

end chapter III

————————————-

Chapter IV

Science-Informed "Theism" (SIT), And Religion

There is no more competition between science and faith than between science and arts or science and tourism.Science is systematized knowledge, whereas faith, arts and tourism and a host of other matters are components of culture, where culture is a ubiquitous biological entity of ALL organisms regardless of size or complexity, selected for survival as the sum total of reactions to and exploitations by the genome of the out-of-cell environments, sensed by the OCM, outer-cell-membrane of the genome, where this OCM is simply and plainly a multi-purpose organ of the in-cell resident communal organism, the genome.

(1) Science's "theism"

– Science's "theism" is An (therefore not The) unknowable undefined source of the energy that constitutes the unknowable undefined Universe.

– The unknowability of the source of cosmic energy, which is also life's matrix, leaves the choice and promotion of our purpose in life to be derived solely from our cognition.

– A term needs to be drawn for a concept and practice of deriving humanity's purpose and course of life. The term should not be related to theism or religion because SIT is NOT founded on faith-belief, and SIT's ethics code is founded on rational commitment and dedication to Life's inherent characteristic, which is cooperation for survival.

(2) Religion, Scientifically

A. Religion, A Human Evolution Definition

From a posting of mine in an evolution discussion forum, written and meant with complete respectful sincerity, at

http://forum.physorg.com/index.php?showtopic=19160&st=0&#entry286766

"A religion is a human artifact for survival of a specific human cultural phenotype, comprising cultural tool-kit and technique ascribed by its adherents to be of higher esteem and benefit than other human cultural survival plans".

B. Sincerely thinking so

Wondering if religious persons who also "accept" science would accept this definition, even with steady unwavering respect and commitment to their religion. IMO such acceptance would contribute respect to religion and to religious persons.

C. Major Conceptual Hierarchies:

– Religion is a progeny of culture, culture being a biological entity, like

– Technology is a progeny of science, like

– Biology is a progeny of life's evolution, like

– Universal Evolution is a progeny of Energy.

D. Uniqueness Of Science Among Human Artifacts

During the recent several centuries in the course of human history Science has been evolving at an accelerating rate as a provider of convincing, ever closer approaching, approximate models of the real world.

We understand that Science is just one of the components of our Culture, our package of capabilities to observe the environment, react to it and exploit it for our satisfaction and survival.

Yet there is a distinct, even if still small, growing spreading tendency to accept the findings of evolving Science with ever increasing respect and appreciation, especially in the realms of all forms and types of technology and of life disciplines.

The crucial 21st century question facing humanity is how much further and into which additional disciplines may or should Science be welcome and adopted by society at large, with what hopes and with what expectations.

end chapter IV

and respectfully resting my case,

Dov Henis

==========================

PS:

I also suggest that general comprehension of evolutionary biology is an essential pre-requisite to the study of cultural anthropology.

– Culture is a basic biological entity. It is a ubiquitous elaboration/extension of genome's activity beyond
its outermost cell membrane and of multicelled organisms' behaviour. It has been selected for survival of the genome as means of extending its exploitation capabilities of the out-of-cell circumstances, consequent to the earlier evolution and selection of the genome's organ, its outermost cell membrane, for controlling the inside-of-cell genes'-commune environmental circumstances.

– Every cultural element is an artifact which involves biological intra-/inter-cell expression and/or process; biological and cultural domains are not ontologically distinct, but instead culture inheres in biology.

– In the case of human cultures, ethnocentrisms are phenotypic cases of anthropocentrism; biologically both are normal Darwinian biological survival phenomena. Thus ethnocultures are human phenotypic survival tools.

DH

====================================

====================================

"Life, Tomorrow's Comprehension" was posted, and displayed few days, in

http://www.nature.com/news/2007/071107/full/450142a.html

Published online 7 November 2007 | Nature 450, 142-143 (2007)

(Attack of the genomes: "How many genome sequences do you need to characterize a model organism? For Drosophila, Heidi Ledford finds, a dozen is a good start.")

After a few days I received the following e-mail from nature.com.:

From: donotreply@nature.com

Sent: Monday, November 12, 2007 To: henisdov@netvision.net.il

Subject: [Nature News] Your post has been hidden

Dear Dov Henis:

The following post you wrote on Nature News has been hidden by the moderator:

" It is about time that "scientists" make the Life Evolution mental leap, that they swallow and digest the revelation that a genome is a living complex organism consisting of (by now) interdependent symbiotic living member genes."

The moderator gave the following reason for this action:

This post does not seem to be about the drosophila genome, or pertinent to the story. Please keep your comments on topic, thanks!

Please refrain from posting similar types of comments on Nature News.

If you would like to dispute this, please email news@nature.com

Thank you.

-Nature News editors

=============================

My response:

Tuesday, November 13, 2007

To: news@nature.com

Subject: Comment on Attack of the genomes, 7 Nov 2007

"If you would like to dispute this, please email news@nature.com "

No dispute, but a comment:

Obviously the removal followed "Could we have a length limit on comments? 10 Nov, 2007, Posted by: Paul Braterman" ( Regents Professor,retd. DH)

I agree with you that criteria for removal of comment should be relevance, not length. But I also suggest that scientific value of the comment be weighed, too, and IMO the length (and even the last para of my comment) could have been forgiven in consideration of the required background for my opening statement "It is about time that "scientists" make the Life Evolution mental leap, that they swallow and digest the revelation that a genome is a living complex organism consisting of (by now) interdependent symbiotic living member genes."

I would even suggest that Nature consider if it might be interested to assess the contents of the comment for another purpose…

Sincerely yours,

Dov henis

============================

Hidden PS questions, Nov 14 2007:

– Is this how scientific issues are discussed/handled in a scientific magazine?

– Does Paul Braterman rhyme with Pouchet ( Pasteur's )?

– With what does Nature News Moderator rhyme ?

DH

====================

Settling A Scientific Issue in nature.com

18 January 2008

Comment On Human Cloning Research

http://www.nature.com/news/2008/080117/full/news.2007.350.html

It is about time that science make the Life Evolution mental leap, that scientists swallow and digest the common-sense realization that it is not cells that are the organisms, that the outer cell membrane is an organ, plain and simple, and that it is the genome that is a living complex organism, consisting of (by now) interdependent symbiotic living member genes.

See http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q–?cq=1&p=372

Therefore there is still a vast empty void of knowledge/experience which is a prerequisite for orderly progress of work on cloning. The still missing required knowledge is the assessment of effects-relationship of the age of the genome-genes on its-their constitution and functioning.

Dov Henis

PS: Following rejection of most of my posted above blog title #372 by Nature News Moderator because 'it's too long', I suspect that I now meet another rejection mode:

When I'm cookie-identified, upon entrance to nature.com, and 'submit' my above comment posting, the reaction is 'Page not found'. I reckon that this time the Nature News Moderator rejects it because the comment is too short…

Dov Henis

============================

On Human Cloning Research, a pleasant surprise

21 Jan 2008

A re-posting trial today in Nature.com went through OK, at

http://www.nature.com/news/2008/080117/full/news.2007.350.html

Relieved.

DH

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